def define_net():
define_net_specific_parameters()
io = ImageIO()
# Read pandas csv labels
y = util.load_labels()
if params.SUBSET is not 0:
y = y[:params.SUBSET]
X = np.arange(y.shape[0])
mean, std = io.load_mean_std(circularized=params.CIRCULARIZED_MEAN_STD)
keys = y.index.values
if params.AUGMENT:
train_iterator = AugmentingParallelBatchIterator(keys, params.BATCH_SIZE, std, mean, y_all = y)
else:
train_iterator = ParallelBatchIterator(keys, params.BATCH_SIZE, std, mean, y_all = y)
test_iterator = ParallelBatchIterator(keys, params.BATCH_SIZE, std, mean, y_all = y)
if params.REGRESSION:
y = util.float32(y)
y = y[:, np.newaxis]
if 'gpu' in theano.config.device:
# Half of coma does not support cuDNN, check whether we can use it on this node
# If not, use cuda_convnet bindings
from theano.sandbox.cuda.dnn import dnn_available
if dnn_available():
from lasagne.layers import dnn
Conv2DLayer = dnn.Conv2DDNNLayer
MaxPool2DLayer = dnn.MaxPool2DDNNLayer
else:
from lasagne.layers import cuda_convnet
Conv2DLayer = cuda_convnet.Conv2DCCLayer
MaxPool2DLayer = cuda_convnet.MaxPool2DCCLayer
else:
Conv2DLayer = layers.Conv2DLayer
MaxPool2DLayer = layers.MaxPool2DLayer
Maxout = layers.pool.FeaturePoolLayer
net = NeuralNet(
layers=[
('input', layers.InputLayer),
('conv0', Conv2DLayer),
('pool0', MaxPool2DLayer),
('conv1', Conv2DLayer),
('pool1', MaxPool2DLayer),
('conv2', Conv2DLayer),
('pool2', MaxPool2DLayer),
('conv3', Conv2DLayer),
('pool3', MaxPool2DLayer),
('conv4', Conv2DLayer),
('pool4', MaxPool2DLayer),
('dropouthidden1', layers.DropoutLayer),
('hidden1', layers.DenseLayer),
('maxout1', Maxout),
('dropouthidden2', layers.DropoutLayer),
('hidden2', layers.DenseLayer),
('maxout2', Maxout),
('dropouthidden3', layers.DropoutLayer),
('output', layers.DenseLayer),
],
input_shape=(None, params.CHANNELS, params.PIXELS, params.PIXELS),
conv0_num_filters=32, conv0_filter_size=(5, 5), conv0_stride=(2, 2), pool0_pool_size=(2, 2), pool0_stride=(2, 2),
conv1_num_filters=64, conv1_filter_size=(5, 5), conv1_border_mode = 'same', pool1_pool_size=(2, 2), pool1_stride=(2, 2),
conv2_num_filters=128, conv2_filter_size=(3, 3), conv2_border_mode = 'same', pool2_pool_size=(2, 2), pool2_stride=(2, 2),
conv3_num_filters=192, conv3_filter_size=(3, 3), conv3_border_mode = 'same', pool3_pool_size=(2, 2), pool3_stride=(2, 2),
conv4_num_filters=256, conv4_filter_size=(3, 3), conv4_border_mode = 'same', pool4_pool_size=(2, 2), pool4_stride=(2, 2),
hidden1_num_units=1024,
hidden2_num_units=1024,
dropouthidden1_p=0.5,
dropouthidden2_p=0.5,
dropouthidden3_p=0.5,
maxout1_pool_size=2,
maxout2_pool_size=2,
output_num_units=1 if params.REGRESSION else 5,
output_nonlinearity=None if params.REGRESSION else nonlinearities.softmax,
update_learning_rate=theano.shared(util.float32(params.START_LEARNING_RATE)),
update_momentum=theano.shared(util.float32(params.MOMENTUM)),
custom_score=('kappa', quadratic_kappa),
regression=params.REGRESSION,
batch_iterator_train=train_iterator,
batch_iterator_test=test_iterator,
on_epoch_finished=[
AdjustVariable('update_learning_rate', start=params.START_LEARNING_RATE),
stats.Stat(),
ModelSaver()
],
max_epochs=500,
verbose=1,
# Only relevant when create_validation_split = True
eval_size=0.1,
# Need to specify splits manually like indicated below!
create_validation_split=params.SUBSET>0,
)
# It is recommended to use the same training/validation split every model for ensembling and threshold optimization
#
# To set specific training/validation split:
net.X_train = np.load(params.IMAGE_SOURCE + "/X_train.npy")
net.X_valid = np.load(params.IMAGE_SOURCE + "/X_valid.npy")
net.y_train = np.load(params.IMAGE_SOURCE + "/y_train.npy")
net.y_valid = np.load(params.IMAGE_SOURCE + "/y_valid.npy")
return net, X, y
def define_net():
define_net_specific_parameters()
io = ImageIO()
# Read pandas csv labels
y = util.load_labels()
if params.SUBSET is not 0:
y = y[:params.SUBSET]
X = np.arange(y.shape[0])
mean, std = io.load_mean_std(circularized=params.CIRCULARIZED_MEAN_STD)
keys = y.index.values
if params.AUGMENT:
train_iterator = AugmentingParallelBatchIterator(keys,
params.BATCH_SIZE,
std,
mean,
y_all=y)
else:
train_iterator = ParallelBatchIterator(keys,
params.BATCH_SIZE,
std,
mean,
y_all=y)
test_iterator = ParallelBatchIterator(keys,
params.BATCH_SIZE,
std,
mean,
y_all=y)
if params.REGRESSION:
y = util.float32(y)
y = y[:, np.newaxis]
if 'gpu' in theano.config.device:
# Half of coma does not support cuDNN, check whether we can use it on this node
# If not, use cuda_convnet bindings
from theano.sandbox.cuda.dnn import dnn_available
if dnn_available() and not params.DISABLE_CUDNN:
from lasagne.layers import dnn
Conv2DLayer = dnn.Conv2DDNNLayer
MaxPool2DLayer = dnn.MaxPool2DDNNLayer
else:
from lasagne.layers import cuda_convnet
Conv2DLayer = cuda_convnet.Conv2DCCLayer
MaxPool2DLayer = cuda_convnet.MaxPool2DCCLayer
else:
Conv2DLayer = layers.Conv2DLayer
MaxPool2DLayer = layers.MaxPool2DLayer
Maxout = layers.pool.FeaturePoolLayer
net = NeuralNet(
layers=[
('input', layers.InputLayer),
('conv0', Conv2DLayer),
('pool0', MaxPool2DLayer),
('conv1', Conv2DLayer),
('pool1', MaxPool2DLayer),
('conv2', Conv2DLayer),
('pool2', MaxPool2DLayer),
('conv3', Conv2DLayer),
('pool3', MaxPool2DLayer),
('conv4', Conv2DLayer),
('pool4', MaxPool2DLayer),
('dropouthidden1', layers.DropoutLayer),
('hidden1', layers.DenseLayer),
('maxout1', Maxout),
('dropouthidden2', layers.DropoutLayer),
('hidden2', layers.DenseLayer),
('maxout2', Maxout),
('dropouthidden3', layers.DropoutLayer),
('output', layers.DenseLayer),
],
input_shape=(None, params.CHANNELS, params.PIXELS, params.PIXELS),
conv0_num_filters=32,
conv0_filter_size=(5, 5),
conv0_stride=(2, 2),
pool0_pool_size=(2, 2),
pool0_stride=(2, 2),
conv1_num_filters=64,
conv1_filter_size=(3, 3),
conv1_border_mode='same',
pool1_pool_size=(2, 2),
pool1_stride=(2, 2),
conv2_num_filters=128,
conv2_filter_size=(3, 3),
conv2_border_mode='same',
pool2_pool_size=(2, 2),
pool2_stride=(2, 2),
conv3_num_filters=192,
conv3_filter_size=(3, 3),
conv3_border_mode='same',
pool3_pool_size=(2, 2),
pool3_stride=(2, 2),
conv4_num_filters=256,
conv4_filter_size=(3, 3),
conv4_border_mode='same',
pool4_pool_size=(2, 2),
pool4_stride=(2, 2),
hidden1_num_units=1024,
hidden2_num_units=1024,
dropouthidden1_p=0.5,
dropouthidden2_p=0.5,
dropouthidden3_p=0.5,
maxout1_pool_size=2,
maxout2_pool_size=2,
output_num_units=1 if params.REGRESSION else 5,
output_nonlinearity=None
if params.REGRESSION else nonlinearities.softmax,
update_learning_rate=theano.shared(
util.float32(params.START_LEARNING_RATE)),
update_momentum=theano.shared(util.float32(params.MOMENTUM)),
custom_score=('kappa', quadratic_kappa),
regression=params.REGRESSION,
batch_iterator_train=train_iterator,
batch_iterator_test=test_iterator,
on_epoch_finished=[
AdjustVariable('update_learning_rate',
start=params.START_LEARNING_RATE),
stats.Stat(),
ModelSaver()
],
max_epochs=500,
verbose=1,
# Only relevant when create_validation_split = True
eval_size=0.1,
# Need to specify splits manually like indicated below!
create_validation_split=params.SUBSET > 0,
)
# It is recommended to use the same training/validation split every model for ensembling and threshold optimization
#
# To set specific training/validation split:
net.X_train = np.load(params.IMAGE_SOURCE + "/X_train.npy")
net.X_valid = np.load(params.IMAGE_SOURCE + "/X_valid.npy")
net.y_train = np.load(params.IMAGE_SOURCE + "/y_train.npy")
net.y_valid = np.load(params.IMAGE_SOURCE + "/y_valid.npy")
return net, X, y
